Starting phenix.real_space_refine on Tue Aug 4 21:33:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10sh_75435/08_2026/10sh_75435.cif Found real_map, /net/cci-nas-00/data/ceres_data/10sh_75435/08_2026/10sh_75435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10sh_75435/08_2026/10sh_75435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10sh_75435/08_2026/10sh_75435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10sh_75435/08_2026/10sh_75435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10sh_75435/08_2026/10sh_75435.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 4836 2.51 5 N 1092 2.21 5 O 1014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6942 Number of models: 1 Model: "" Number of chains: 234 Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "v" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AC" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AC" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AD" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AE" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AF" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AG" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AH" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AI" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AJ" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AK" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AK" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AM" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AO" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AE" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AF" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AG" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AH" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AI" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AJ" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AK" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AL" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AM" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AN" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AO" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AP" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'DAO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.09, per 1000 atoms: 0.30 Number of scatterers: 6942 At special positions: 0 Unit cell: (93.896, 105.536, 54.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1014 8.00 N 1092 7.00 C 4836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=156, symmetry=0 Number of additional bonds: simple=156, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 324.6 milliseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.28: 852 1.28 - 1.35: 815 1.35 - 1.42: 895 1.42 - 1.50: 1092 1.50 - 1.57: 3288 Bond restraints: 6942 Sorted by residual: bond pdb=" C ILE 7 7 " pdb=" N GLY 7 8 " ideal model delta sigma weight residual 1.331 1.358 -0.027 6.60e-03 2.30e+04 1.63e+01 bond pdb=" C ILE S 7 " pdb=" N GLY S 8 " ideal model delta sigma weight residual 1.331 1.358 -0.027 6.60e-03 2.30e+04 1.63e+01 bond pdb=" C ILE l 7 " pdb=" N GLY l 8 " ideal model delta sigma weight residual 1.331 1.357 -0.026 6.60e-03 2.30e+04 1.61e+01 bond pdb=" C ILEAL 7 " pdb=" N GLYAL 8 " ideal model delta sigma weight residual 1.331 1.357 -0.026 6.60e-03 2.30e+04 1.59e+01 bond pdb=" C ILE y 7 " pdb=" N GLY y 8 " ideal model delta sigma weight residual 1.331 1.357 -0.026 6.60e-03 2.30e+04 1.55e+01 ... (remaining 6937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 6842 2.04 - 4.08: 1803 4.08 - 6.11: 205 6.11 - 8.15: 36 8.15 - 10.19: 6 Bond angle restraints: 8892 Sorted by residual: angle pdb=" C HIS m 2 " pdb=" N TYR m 3 " pdb=" CA TYR m 3 " ideal model delta sigma weight residual 123.10 128.27 -5.17 9.60e-01 1.09e+00 2.90e+01 angle pdb=" C HIS z 2 " pdb=" N TYR z 3 " pdb=" CA TYR z 3 " ideal model delta sigma weight residual 123.10 128.25 -5.15 9.60e-01 1.09e+00 2.88e+01 angle pdb=" C LYS m 11 " pdb=" CA LYS m 11 " pdb=" CB LYS m 11 " ideal model delta sigma weight residual 110.10 120.29 -10.19 1.90e+00 2.77e-01 2.88e+01 angle pdb=" C LYS T 11 " pdb=" CA LYS T 11 " pdb=" CB LYS T 11 " ideal model delta sigma weight residual 110.10 120.28 -10.18 1.90e+00 2.77e-01 2.87e+01 angle pdb=" C LYS z 11 " pdb=" CA LYS z 11 " pdb=" CB LYS z 11 " ideal model delta sigma weight residual 110.10 120.28 -10.18 1.90e+00 2.77e-01 2.87e+01 ... (remaining 8887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.28: 3384 9.28 - 18.55: 494 18.55 - 27.83: 172 27.83 - 37.10: 48 37.10 - 46.38: 36 Dihedral angle restraints: 4134 sinusoidal: 2106 harmonic: 2028 Sorted by residual: dihedral pdb=" CA ILE v 7 " pdb=" C ILE v 7 " pdb=" N GLY v 8 " pdb=" CA GLY v 8 " ideal model delta harmonic sigma weight residual -180.00 -154.52 -25.48 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ILE G 7 " pdb=" C ILE G 7 " pdb=" N GLY G 8 " pdb=" CA GLY G 8 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ILE O 7 " pdb=" C ILE O 7 " pdb=" N GLY O 8 " pdb=" CA GLY O 8 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 4131 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.058: 258 0.058 - 0.115: 315 0.115 - 0.172: 105 0.172 - 0.229: 151 0.229 - 0.286: 29 Chirality restraints: 858 Sorted by residual: chirality pdb=" CA PROAO 4 " pdb=" N PROAO 4 " pdb=" C PROAO 4 " pdb=" CB PROAO 4 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA PROAB 4 " pdb=" N PROAB 4 " pdb=" C PROAB 4 " pdb=" CB PROAB 4 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA PRO b 4 " pdb=" N PRO b 4 " pdb=" C PRO b 4 " pdb=" CB PRO b 4 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 855 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY w 9 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C GLY w 9 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY w 9 " -0.019 2.00e-02 2.50e+03 pdb=" N SER w 10 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY I 9 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C GLY I 9 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY I 9 " -0.019 2.00e-02 2.50e+03 pdb=" N SER I 10 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYAJ 9 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C GLYAJ 9 " 0.049 2.00e-02 2.50e+03 pdb=" O GLYAJ 9 " -0.019 2.00e-02 2.50e+03 pdb=" N SERAJ 10 " -0.017 2.00e-02 2.50e+03 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 2498 2.93 - 3.42: 5760 3.42 - 3.92: 11771 3.92 - 4.41: 15002 4.41 - 4.90: 26674 Nonbonded interactions: 61705 Sorted by model distance: nonbonded pdb=" CB SER D 10 " pdb=" O GLY n 8 " model vdw 2.440 3.440 nonbonded pdb=" O GLYAA 8 " pdb=" CB SERAD 10 " model vdw 2.440 3.440 nonbonded pdb=" O GLY U 8 " pdb=" CB SER X 10 " model vdw 2.440 3.440 nonbonded pdb=" O GLY a 8 " pdb=" CB SER d 10 " model vdw 2.440 3.440 nonbonded pdb=" O GLY Y 8 " pdb=" CB SER q 10 " model vdw 2.441 3.440 ... (remaining 61700 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'AE' selection = chain 'AF' selection = chain 'AG' selection = chain 'AH' selection = chain 'AI' selection = chain 'AJ' selection = chain 'AK' selection = chain 'AL' selection = chain 'AM' selection = chain 'AN' selection = chain 'AO' selection = chain 'AP' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.780 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.193 7098 Z= 2.233 Angle : 1.840 10.188 8892 Z= 1.158 Chirality : 0.121 0.286 858 Planarity : 0.008 0.029 936 Dihedral : 10.666 46.379 2886 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.42 % Favored : 85.58 % Rotamer: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.56 (0.23), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.17), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.006 TYR i 3 HIS 0.010 0.003 HIS t 2 Details of bonding type rmsd/Z covalent geometry : bond 0.01299 / 0.84 ( 6942) covalent geometry : angle 1.84036 / 1.16 ( 8892) Misc. bond : bond 0.13974 / 9.71 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: R 2 HIS cc_start: 0.2266 (t-90) cc_final: 0.1699 (t-170) REVERT: Z 4 PRO cc_start: 0.6643 (Cg_endo) cc_final: 0.6379 (Cg_exo) REVERT: 8 3 TYR cc_start: 0.8602 (m-10) cc_final: 0.7977 (m-10) REVERT: V 4 PRO cc_start: 0.6828 (Cg_endo) cc_final: 0.6592 (Cg_exo) REVERT: b 4 PRO cc_start: 0.6739 (Cg_endo) cc_final: 0.6435 (Cg_exo) REVERT: h 10 SER cc_start: 0.9316 (p) cc_final: 0.9109 (p) REVERT: o 4 PRO cc_start: 0.6429 (Cg_endo) cc_final: 0.6159 (Cg_exo) REVERT: AC 3 TYR cc_start: 0.8422 (m-10) cc_final: 0.7960 (m-10) REVERT: AK 2 HIS cc_start: 0.3291 (t-90) cc_final: 0.3004 (t70) REVERT: AP 3 TYR cc_start: 0.8012 (m-10) cc_final: 0.7796 (m-10) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0733 time to fit residues: 11.1418 Evaluate side-chains 58 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 2 HIS ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 2 HIS ** j 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 2 HIS r 2 HIS ** w 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.144697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.113866 restraints weight = 12280.797| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 3.70 r_work: 0.3900 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 7098 Z= 0.286 Angle : 0.806 6.019 8892 Z= 0.389 Chirality : 0.063 0.133 858 Planarity : 0.005 0.051 936 Dihedral : 7.609 58.505 1560 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.88 % Allowed : 14.42 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.82 (0.25), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.19), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.003 TYR L 3 HIS 0.008 0.002 HISAB 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.29 ( 6942) covalent geometry : angle 0.80616 / 0.39 ( 8892) Misc. bond : bond 0.00172 / 0.12 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.249 Fit side-chains REVERT: D 3 TYR cc_start: 0.7266 (m-10) cc_final: 0.7008 (m-80) REVERT: O 3 TYR cc_start: 0.5902 (OUTLIER) cc_final: 0.5045 (m-80) REVERT: 8 3 TYR cc_start: 0.7790 (m-10) cc_final: 0.6776 (m-10) REVERT: c 3 TYR cc_start: 0.7776 (m-10) cc_final: 0.7388 (m-10) REVERT: d 3 TYR cc_start: 0.7260 (m-80) cc_final: 0.6932 (m-80) REVERT: i 3 TYR cc_start: 0.5749 (OUTLIER) cc_final: 0.5078 (m-80) REVERT: p 3 TYR cc_start: 0.7760 (m-10) cc_final: 0.6995 (m-10) REVERT: v 3 TYR cc_start: 0.6019 (OUTLIER) cc_final: 0.4966 (m-80) REVERT: AI 3 TYR cc_start: 0.6204 (OUTLIER) cc_final: 0.5675 (m-80) outliers start: 18 outliers final: 6 residues processed: 82 average time/residue: 0.0815 time to fit residues: 8.7717 Evaluate side-chains 51 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 TYR Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain i residue 3 TYR Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain v residue 3 TYR Chi-restraints excluded: chain AI residue 3 TYR Chi-restraints excluded: chain AP residue 10 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 15 optimal weight: 10.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 2 HIS ** K 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 2 HIS ** 5 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 2 HIS ** j 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 2 HIS ** t 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.144113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.113120 restraints weight = 12174.285| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 3.78 r_work: 0.3885 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7098 Z= 0.204 Angle : 0.677 5.799 8892 Z= 0.321 Chirality : 0.064 0.134 858 Planarity : 0.005 0.069 936 Dihedral : 7.701 46.947 1560 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.04 % Allowed : 15.22 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.45 (0.26), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR X 3 HIS 0.010 0.001 HISAB 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 ( 6942) covalent geometry : angle 0.67701 / 0.32 ( 8892) Misc. bond : bond 0.00070 / 0.05 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.340 Fit side-chains REVERT: D 3 TYR cc_start: 0.7092 (m-10) cc_final: 0.6818 (m-80) REVERT: O 3 TYR cc_start: 0.5801 (OUTLIER) cc_final: 0.4985 (m-80) REVERT: 8 3 TYR cc_start: 0.7595 (m-10) cc_final: 0.6518 (m-10) REVERT: W 3 TYR cc_start: 0.7438 (m-10) cc_final: 0.7127 (m-10) REVERT: 1 3 TYR cc_start: 0.7113 (m-80) cc_final: 0.6902 (m-80) REVERT: 9 3 TYR cc_start: 0.6656 (OUTLIER) cc_final: 0.5993 (m-80) REVERT: c 3 TYR cc_start: 0.7667 (m-10) cc_final: 0.6857 (m-10) REVERT: d 3 TYR cc_start: 0.7305 (m-80) cc_final: 0.7068 (m-80) REVERT: i 3 TYR cc_start: 0.5691 (OUTLIER) cc_final: 0.5047 (m-80) REVERT: p 3 TYR cc_start: 0.7560 (m-10) cc_final: 0.6781 (m-10) REVERT: v 3 TYR cc_start: 0.5872 (OUTLIER) cc_final: 0.4863 (m-80) REVERT: AI 3 TYR cc_start: 0.6026 (OUTLIER) cc_final: 0.5545 (m-80) outliers start: 19 outliers final: 9 residues processed: 77 average time/residue: 0.0790 time to fit residues: 8.1814 Evaluate side-chains 63 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 9 residue 3 TYR Chi-restraints excluded: chain b residue 2 HIS Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain i residue 3 TYR Chi-restraints excluded: chain i residue 10 SER Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain v residue 3 TYR Chi-restraints excluded: chain AB residue 10 SER Chi-restraints excluded: chain AI residue 3 TYR Chi-restraints excluded: chain AP residue 10 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 0.1980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 2 HIS ** 5 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 2 HIS ** j 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 2 HIS ** t 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.144342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.113276 restraints weight = 12250.206| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.75 r_work: 0.3878 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7098 Z= 0.191 Angle : 0.644 5.310 8892 Z= 0.304 Chirality : 0.063 0.132 858 Planarity : 0.005 0.064 936 Dihedral : 7.462 42.982 1560 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.88 % Allowed : 14.90 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.22 (0.27), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR T 3 HIS 0.008 0.001 HISAB 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 ( 6942) covalent geometry : angle 0.64364 / 0.30 ( 8892) Misc. bond : bond 0.00107 / 0.07 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.184 Fit side-chains REVERT: D 3 TYR cc_start: 0.7192 (m-80) cc_final: 0.6959 (m-80) REVERT: O 3 TYR cc_start: 0.5859 (OUTLIER) cc_final: 0.5018 (m-80) REVERT: 8 3 TYR cc_start: 0.7589 (m-10) cc_final: 0.6501 (m-10) REVERT: A 3 TYR cc_start: 0.7496 (m-10) cc_final: 0.6734 (m-80) REVERT: W 3 TYR cc_start: 0.7454 (m-10) cc_final: 0.7171 (m-10) REVERT: 9 3 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.6058 (m-80) REVERT: c 3 TYR cc_start: 0.7646 (m-10) cc_final: 0.6837 (m-10) REVERT: i 3 TYR cc_start: 0.5761 (OUTLIER) cc_final: 0.5045 (m-80) REVERT: p 3 TYR cc_start: 0.7577 (m-10) cc_final: 0.6786 (m-10) REVERT: v 3 TYR cc_start: 0.5973 (OUTLIER) cc_final: 0.4934 (m-80) REVERT: AI 3 TYR cc_start: 0.6095 (OUTLIER) cc_final: 0.5659 (m-80) outliers start: 18 outliers final: 8 residues processed: 75 average time/residue: 0.0776 time to fit residues: 7.5898 Evaluate side-chains 57 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 TYR Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 9 residue 3 TYR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain i residue 3 TYR Chi-restraints excluded: chain o residue 2 HIS Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain v residue 3 TYR Chi-restraints excluded: chain AI residue 3 TYR Chi-restraints excluded: chain AP residue 10 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 overall best weight: 5.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 2 HIS ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 HIS ** E 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 HIS ** 5 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 2 HIS e 2 HIS ** g 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 2 HIS ** t 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 2 HIS ** AG 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 2 HIS ** AI 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 2 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.141737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.110537 restraints weight = 12446.001| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 3.68 r_work: 0.3840 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 7098 Z= 0.305 Angle : 0.801 6.046 8892 Z= 0.382 Chirality : 0.067 0.184 858 Planarity : 0.006 0.057 936 Dihedral : 9.664 59.982 1560 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.37 % Allowed : 16.03 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.27), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.003 TYR f 3 HIS 0.008 0.001 HIS K 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.31 ( 6942) covalent geometry : angle 0.80129 / 0.38 ( 8892) Misc. bond : bond 0.00135 / 0.09 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.306 Fit side-chains REVERT: O 3 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.5058 (m-80) REVERT: R 3 TYR cc_start: 0.6632 (m-80) cc_final: 0.6411 (m-80) REVERT: 8 3 TYR cc_start: 0.7616 (m-10) cc_final: 0.6565 (m-10) REVERT: A 3 TYR cc_start: 0.7564 (m-10) cc_final: 0.6821 (m-80) REVERT: 7 3 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: 9 3 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.6152 (m-80) REVERT: c 3 TYR cc_start: 0.7744 (m-10) cc_final: 0.7354 (m-10) REVERT: i 3 TYR cc_start: 0.5819 (OUTLIER) cc_final: 0.5089 (m-80) REVERT: p 3 TYR cc_start: 0.7636 (m-10) cc_final: 0.6852 (m-10) REVERT: v 3 TYR cc_start: 0.6012 (OUTLIER) cc_final: 0.4946 (m-80) REVERT: AC 3 TYR cc_start: 0.7662 (m-10) cc_final: 0.6725 (m-10) REVERT: AG 3 TYR cc_start: 0.7420 (m-80) cc_final: 0.7001 (t80) REVERT: AI 3 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.5637 (m-80) outliers start: 21 outliers final: 12 residues processed: 71 average time/residue: 0.0872 time to fit residues: 8.0700 Evaluate side-chains 62 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 TYR Chi-restraints excluded: chain N residue 3 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 7 residue 3 TYR Chi-restraints excluded: chain 9 residue 3 TYR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain i residue 3 TYR Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain o residue 2 HIS Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain v residue 3 TYR Chi-restraints excluded: chain y residue 3 TYR Chi-restraints excluded: chain AB residue 10 SER Chi-restraints excluded: chain AI residue 3 TYR Chi-restraints excluded: chain AP residue 3 TYR Chi-restraints excluded: chain AP residue 10 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 2 HIS ** g 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AG 2 HIS ** AI 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.141391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.110110 restraints weight = 12449.714| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 3.68 r_work: 0.3839 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 7098 Z= 0.307 Angle : 0.761 5.845 8892 Z= 0.365 Chirality : 0.066 0.132 858 Planarity : 0.006 0.053 936 Dihedral : 9.483 56.974 1560 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.69 % Allowed : 15.38 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.27), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR T 3 HIS 0.007 0.001 HIS J 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.31 ( 6942) covalent geometry : angle 0.76142 / 0.37 ( 8892) Misc. bond : bond 0.00133 / 0.09 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.169 Fit side-chains REVERT: O 3 TYR cc_start: 0.6009 (OUTLIER) cc_final: 0.5103 (m-80) REVERT: 8 3 TYR cc_start: 0.7621 (m-10) cc_final: 0.6549 (m-10) REVERT: A 3 TYR cc_start: 0.7673 (m-80) cc_final: 0.6808 (m-80) REVERT: C 3 TYR cc_start: 0.6090 (m-80) cc_final: 0.5865 (p90) REVERT: 7 3 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: 9 3 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.6198 (m-80) REVERT: c 3 TYR cc_start: 0.7741 (m-10) cc_final: 0.7325 (m-10) REVERT: i 3 TYR cc_start: 0.5780 (OUTLIER) cc_final: 0.5044 (m-80) REVERT: l 3 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: p 3 TYR cc_start: 0.7619 (m-10) cc_final: 0.6807 (m-10) REVERT: v 3 TYR cc_start: 0.6001 (OUTLIER) cc_final: 0.4943 (m-80) REVERT: AC 3 TYR cc_start: 0.7640 (m-10) cc_final: 0.6749 (m-10) REVERT: AG 3 TYR cc_start: 0.7364 (m-80) cc_final: 0.6970 (t80) REVERT: AI 3 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.5644 (m-80) outliers start: 23 outliers final: 12 residues processed: 71 average time/residue: 0.0798 time to fit residues: 7.3145 Evaluate side-chains 63 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 TYR Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain 8 residue 10 SER Chi-restraints excluded: chain N residue 3 TYR Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 7 residue 3 TYR Chi-restraints excluded: chain 9 residue 3 TYR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain i residue 3 TYR Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain o residue 2 HIS Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain v residue 3 TYR Chi-restraints excluded: chain v residue 10 SER Chi-restraints excluded: chain y residue 3 TYR Chi-restraints excluded: chain AI residue 3 TYR Chi-restraints excluded: chain AP residue 3 TYR Chi-restraints excluded: chain AP residue 10 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.0770 chunk 68 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.0070 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 2 HIS ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.146543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.116191 restraints weight = 12269.957| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 3.78 r_work: 0.3940 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7098 Z= 0.097 Angle : 0.552 4.304 8892 Z= 0.262 Chirality : 0.062 0.130 858 Planarity : 0.005 0.052 936 Dihedral : 7.292 50.503 1560 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.56 % Allowed : 16.99 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.29), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR T 3 HIS 0.003 0.000 HISAB 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 6942) covalent geometry : angle 0.55185 / 0.26 ( 8892) Misc. bond : bond 0.00020 / 0.01 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.263 Fit side-chains REVERT: O 3 TYR cc_start: 0.5721 (OUTLIER) cc_final: 0.4961 (m-80) REVERT: 8 3 TYR cc_start: 0.7382 (m-10) cc_final: 0.6332 (m-10) REVERT: A 3 TYR cc_start: 0.7512 (m-80) cc_final: 0.6580 (m-80) REVERT: 7 3 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: c 3 TYR cc_start: 0.7561 (m-10) cc_final: 0.7173 (m-10) REVERT: i 3 TYR cc_start: 0.5628 (OUTLIER) cc_final: 0.5031 (m-80) REVERT: j 3 TYR cc_start: 0.6033 (m-80) cc_final: 0.5687 (t80) REVERT: l 3 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: p 3 TYR cc_start: 0.7466 (m-10) cc_final: 0.6577 (m-10) REVERT: v 3 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.4895 (m-80) REVERT: AC 3 TYR cc_start: 0.7482 (m-10) cc_final: 0.6596 (m-10) REVERT: AG 3 TYR cc_start: 0.7274 (m-80) cc_final: 0.6848 (t80) outliers start: 16 outliers final: 8 residues processed: 72 average time/residue: 0.0940 time to fit residues: 8.7060 Evaluate side-chains 60 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 TYR Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain N residue 3 TYR Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 7 residue 3 TYR Chi-restraints excluded: chain i residue 3 TYR Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain v residue 3 TYR Chi-restraints excluded: chain y residue 3 TYR Chi-restraints excluded: chain AB residue 10 SER Chi-restraints excluded: chain AL residue 3 TYR Chi-restraints excluded: chain AP residue 3 TYR Chi-restraints excluded: chain AP residue 10 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 51 optimal weight: 0.1980 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 2 HIS ** w 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.143313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.112592 restraints weight = 12397.055| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 3.73 r_work: 0.3870 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 7098 Z= 0.275 Angle : 0.729 5.626 8892 Z= 0.350 Chirality : 0.065 0.130 858 Planarity : 0.006 0.052 936 Dihedral : 8.751 59.182 1560 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.04 % Allowed : 17.79 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.28), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.002 TYR T 3 HIS 0.004 0.001 HIS B 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.28 ( 6942) covalent geometry : angle 0.72914 / 0.35 ( 8892) Misc. bond : bond 0.00121 / 0.08 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.256 Fit side-chains REVERT: O 3 TYR cc_start: 0.5777 (OUTLIER) cc_final: 0.4854 (m-80) REVERT: 8 3 TYR cc_start: 0.7490 (m-10) cc_final: 0.6451 (m-10) REVERT: A 3 TYR cc_start: 0.7633 (m-80) cc_final: 0.6719 (m-80) REVERT: 7 3 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: 9 3 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.6239 (m-80) REVERT: c 3 TYR cc_start: 0.7704 (m-10) cc_final: 0.7316 (m-10) REVERT: i 3 TYR cc_start: 0.5689 (OUTLIER) cc_final: 0.4973 (m-80) REVERT: l 3 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: p 3 TYR cc_start: 0.7539 (m-10) cc_final: 0.6760 (m-10) REVERT: v 3 TYR cc_start: 0.5913 (OUTLIER) cc_final: 0.4916 (m-80) REVERT: AC 3 TYR cc_start: 0.7598 (m-10) cc_final: 0.6721 (m-10) REVERT: AK 3 TYR cc_start: 0.6961 (m-80) cc_final: 0.6511 (t80) outliers start: 19 outliers final: 11 residues processed: 68 average time/residue: 0.1005 time to fit residues: 8.8486 Evaluate side-chains 60 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 TYR Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain 8 residue 10 SER Chi-restraints excluded: chain N residue 3 TYR Chi-restraints excluded: chain V residue 2 HIS Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 7 residue 3 TYR Chi-restraints excluded: chain 9 residue 3 TYR Chi-restraints excluded: chain i residue 3 TYR Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain v residue 3 TYR Chi-restraints excluded: chain y residue 3 TYR Chi-restraints excluded: chain AB residue 10 SER Chi-restraints excluded: chain AP residue 3 TYR Chi-restraints excluded: chain AP residue 10 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 66 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.144579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.113946 restraints weight = 12461.047| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 3.75 r_work: 0.3894 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7098 Z= 0.175 Angle : 0.628 4.885 8892 Z= 0.301 Chirality : 0.063 0.146 858 Planarity : 0.006 0.052 936 Dihedral : 8.025 57.534 1560 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.72 % Allowed : 18.11 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.29), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR T 3 HIS 0.002 0.001 HIS R 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 6942) covalent geometry : angle 0.62756 / 0.30 ( 8892) Misc. bond : bond 0.00076 / 0.05 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.291 Fit side-chains REVERT: O 3 TYR cc_start: 0.5790 (OUTLIER) cc_final: 0.4990 (m-80) REVERT: 8 3 TYR cc_start: 0.7430 (m-10) cc_final: 0.6393 (m-10) REVERT: A 3 TYR cc_start: 0.7566 (m-80) cc_final: 0.6658 (m-80) REVERT: 7 3 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: c 3 TYR cc_start: 0.7620 (m-10) cc_final: 0.7198 (m-10) REVERT: i 3 TYR cc_start: 0.5740 (OUTLIER) cc_final: 0.5084 (m-80) REVERT: j 3 TYR cc_start: 0.6053 (m-80) cc_final: 0.5695 (t80) REVERT: l 3 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: p 3 TYR cc_start: 0.7522 (m-10) cc_final: 0.6674 (m-10) REVERT: v 3 TYR cc_start: 0.5864 (OUTLIER) cc_final: 0.4898 (m-80) REVERT: AC 3 TYR cc_start: 0.7542 (m-10) cc_final: 0.6646 (m-10) REVERT: AK 3 TYR cc_start: 0.6888 (m-80) cc_final: 0.6476 (t80) REVERT: AL 3 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.6999 (m-80) REVERT: AM 3 TYR cc_start: 0.6929 (m-80) cc_final: 0.6716 (m-10) outliers start: 17 outliers final: 10 residues processed: 69 average time/residue: 0.1067 time to fit residues: 9.3835 Evaluate side-chains 65 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 TYR Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain 8 residue 10 SER Chi-restraints excluded: chain N residue 3 TYR Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 7 residue 3 TYR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain i residue 3 TYR Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain v residue 3 TYR Chi-restraints excluded: chain y residue 3 TYR Chi-restraints excluded: chain AB residue 10 SER Chi-restraints excluded: chain AL residue 3 TYR Chi-restraints excluded: chain AP residue 3 TYR Chi-restraints excluded: chain AP residue 10 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 2 optimal weight: 10.9990 chunk 34 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.143745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.112776 restraints weight = 12612.153| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 3.76 r_work: 0.3887 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7098 Z= 0.216 Angle : 0.690 5.396 8892 Z= 0.330 Chirality : 0.064 0.149 858 Planarity : 0.006 0.055 936 Dihedral : 8.472 57.011 1560 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.72 % Allowed : 18.43 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.28), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.002 TYR 9 3 HIS 0.010 0.001 HISAF 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 ( 6942) covalent geometry : angle 0.68975 / 0.33 ( 8892) Misc. bond : bond 0.00094 / 0.07 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.176 Fit side-chains REVERT: O 3 TYR cc_start: 0.5859 (OUTLIER) cc_final: 0.4934 (m-80) REVERT: 8 3 TYR cc_start: 0.7440 (m-10) cc_final: 0.6393 (m-10) REVERT: A 3 TYR cc_start: 0.7591 (m-80) cc_final: 0.6723 (m-80) REVERT: M 3 TYR cc_start: 0.7025 (m-80) cc_final: 0.6803 (m-80) REVERT: 7 3 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: c 3 TYR cc_start: 0.7656 (m-10) cc_final: 0.7268 (m-10) REVERT: i 3 TYR cc_start: 0.5752 (OUTLIER) cc_final: 0.5026 (m-80) REVERT: j 3 TYR cc_start: 0.6104 (m-80) cc_final: 0.5751 (t80) REVERT: l 3 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: p 3 TYR cc_start: 0.7551 (m-10) cc_final: 0.6744 (m-10) REVERT: v 3 TYR cc_start: 0.5878 (OUTLIER) cc_final: 0.4888 (m-80) REVERT: AC 3 TYR cc_start: 0.7561 (m-10) cc_final: 0.6651 (m-10) REVERT: AF 3 TYR cc_start: 0.6953 (m-80) cc_final: 0.6717 (m-10) REVERT: AK 3 TYR cc_start: 0.6827 (m-80) cc_final: 0.6390 (t80) REVERT: AL 3 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7029 (m-80) outliers start: 17 outliers final: 10 residues processed: 68 average time/residue: 0.1033 time to fit residues: 8.9526 Evaluate side-chains 65 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 TYR Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain 8 residue 10 SER Chi-restraints excluded: chain N residue 3 TYR Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 7 residue 3 TYR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain i residue 3 TYR Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain v residue 3 TYR Chi-restraints excluded: chain y residue 3 TYR Chi-restraints excluded: chain AB residue 10 SER Chi-restraints excluded: chain AL residue 3 TYR Chi-restraints excluded: chain AP residue 3 TYR Chi-restraints excluded: chain AP residue 10 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.141674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.111007 restraints weight = 12656.371| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.68 r_work: 0.3864 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 7098 Z= 0.312 Angle : 0.807 6.119 8892 Z= 0.388 Chirality : 0.068 0.147 858 Planarity : 0.006 0.053 936 Dihedral : 9.757 59.858 1560 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 3.53 % Allowed : 17.63 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.91 (0.28), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.002 TYR 1 3 HIS 0.008 0.001 HIS T 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.31 ( 6942) covalent geometry : angle 0.80684 / 0.39 ( 8892) Misc. bond : bond 0.00141 / 0.10 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1375.01 seconds wall clock time: 24 minutes 33.92 seconds (1473.92 seconds total)